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- PDB-8b7f: Nuclease from C. glutamicum -

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Basic information

Entry
Database: PDB / ID: 8b7f
TitleNuclease from C. glutamicum
ComponentsUbiquitin-like protein SMT3,MksG
KeywordsMETAL BINDING PROTEIN / Nuclease
Function / homology
Function and homology information


SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / condensed nuclear chromosome / PML body / protein tag activity / identical protein binding / nucleus
Similarity search - Function
Uncharacterised conserved protein UCP028408 / Wadjet protein JetD, C-terminal / Domain of unknown function DUF3322 / Wadjet protein JetD, C-terminal / Uncharacterized protein conserved in bacteria N-term (DUF3322) / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-like protein SMT3 / DUF3322 and DUF2220 domain-containing protein
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.6 Å
AuthorsWehenkel, A. / Ben Assaya, M. / Haouz, A.
Funding support France, 1items
OrganizationGrant numberCountry
Pasteur Institute France
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG.
Authors: Weiss, M. / Giacomelli, G. / Assaya, M.B. / Grundt, F. / Haouz, A. / Peng, F. / Petrella, S. / Wehenkel, A.M. / Bramkamp, M.
History
DepositionSep 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-like protein SMT3,MksG
B: Ubiquitin-like protein SMT3,MksG


Theoretical massNumber of molelcules
Total (without water)107,3072
Polymers107,3072
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.086, 126.776, 150.111
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 21 through 215)
d_2ens_1(chain "B" and resid 21 through 215)
d_1ens_2(chain "A" and resid 219 through 388)
d_2ens_2(chain "B" and resid 219 through 388)

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1METMETASPASPAA21 - 215107 - 301
d_2ens_1METMETASPASPBB21 - 215107 - 301
d_1ens_2ARGARGGLYGLYAA219 - 388305 - 474
d_2ens_2ARGARGGLYGLYBB219 - 388305 - 474

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.8505595672, -0.0174916185267, 0.525587733805), (-0.00837781349288, -0.998869132327, -0.0468003068894), (0.525811976742, -0.0442097247806, 0.849451155364)52.6042394354, 103.340566177, -12.8422212867
2given(-0.786437613061, -0.0259318917537, 0.617125123256), (0.00290837722281, -0.999262697761, -0.0382831843665), (0.617662870914, -0.0283125034814, 0.785933190571)48.9761005045, 102.37914323, -14.5249204985

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Components

#1: Protein Ubiquitin-like protein SMT3,MksG


Mass: 53653.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 204508 / S288c, ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: SMT3, YDR510W, D9719.15, Cgl2803 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12306, UniProt: Q8NLY3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% (w/v) PEG 6K, 30% (v/v) ethanol and 10 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 4.6→61.5 Å / Num. obs: 8738 / % possible obs: 99.5 % / Redundancy: 13.1 % / Biso Wilson estimate: 136.52 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.054 / Net I/σ(I): 9.6
Reflection shellResolution: 4.6→4.77 Å / Num. unique obs: 597 / CC1/2: 0.816 / Rpim(I) all: 0.444

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487-000refinement
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 4.6→49.21 Å / SU ML: 0.7117 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.2601
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3114 393 5.17 %
Rwork0.2695 7202 -
obs0.2717 7595 87.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 146.84 Å2
Refinement stepCycle: LAST / Resolution: 4.6→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5862 0 0 0 5862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00385998
X-RAY DIFFRACTIONf_angle_d0.88758158
X-RAY DIFFRACTIONf_chiral_restr0.0506914
X-RAY DIFFRACTIONf_plane_restr0.01141058
X-RAY DIFFRACTIONf_dihedral_angle_d5.3998800
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONcartesian NCS0.0596945755362
ens_2d_2AX-RAY DIFFRACTIONcartesian NCS0.0429574247351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.6-5.270.37281030.33441855X-RAY DIFFRACTION69.02
5.27-6.630.39511280.32772519X-RAY DIFFRACTION92.23
6.64-49.210.26091620.2262828X-RAY DIFFRACTION99.6
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.011494511232.768891334026.585520107081.511568300534.548708947328.475977773980.458818337795-0.296582554511-0.2777414774220.159082103406-0.282622229815-0.3016221558290.361029701667-0.657657277123-0.02111700581510.790814488816-0.103252782547-0.04432624183511.18790049992-0.104725330080.74954067986512.057631903614.71388978978.18998304404
24.64133741877-0.6541448582892.631900808353.65581988716-1.333393294384.83738239464-0.143609842668-0.0172689908275-0.06655625976020.517170607725-0.1661810536840.5247775130010.00750431906073-0.266759687260.1134859876251.028669942780.03726492248950.249409108660.795785290406-0.2704035638920.88488300241326.659051283564.990557433338.1574120823
31.057903794560.514102617529-0.4497598161351.07801015532-1.606998655676.099635069910.2807468556121.10011974730.0948205922774-0.55232012091-0.463154990879-0.599720885591-1.214095796580.2636013550810.3749937099191.68191571435-0.02727765797150.2028602627651.62909125230.2090737889240.73265216503346.39557305688.1591210415-0.19571289784
41.263376499972.130873922060.1476447823387.012570682332.544324998137.51517974809-0.05509924985490.22461163829-0.579972459443-0.498668389320.187701272732-0.444539600311-0.280275492076-0.0850708414638-0.3091864156870.9474373757730.123681140162-0.01422439153581.068227523610.03460365409730.95995595955949.872979368236.053276413530.0904433539
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 21 through 215 )AA21 - 2151 - 195
22chain 'A' and (resid 219 through 388 )AA219 - 388199 - 368
33chain 'B' and (resid 21 through 215 )BB21 - 2151 - 195
44chain 'B' and (resid 219 through 388 )BB219 - 388199 - 368

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